OPTIONS FOR ANALYZING UNBALANCED SPLIT-PLOT EXPERIMENTS: A CASE STUDY

Unbalanced split-plot experiments present many analysis problems. This paper discusses some of the difficulties by comparing the results of the analysis recommended by Milliken and Johnson (1984) to a set of minimal sufficient statistics using a small experiment from Milliken and Johnson as a case study. The estimators used by Milliken and Johnson are not necessarily the best (smallest variance) estimators. A set of minimal sufficient statistics is used to show that the whole plot error term suggested by Milliken and Johnson does not have a distribution that is proportional to an exact chi-square distribution and is not always independent of parameter function estimators. Other options for analyzing unbalanced split-plot experiments and unbalanced repeated measures experiments in which the repeated measures satisfy the Huyhn-Feldt (1970) conditions are proposed

VARIANCE INFLATION FACTORS IN REGRESSION MODELS WITH DUMMY VARIABLES

Variance Inflation Factors (VIFs) are used to detect collinearity among predictors in regression models. Textbook explanation of collinearity and diagnostics such as VIFs have focused on numeric predictors as being co-linear or co-planar , with little attention paid to VIFs when a dummy variable is included in the model. This work was motivated by two regression models with high VIFs, where standard\u27 interpretations of causes of collinearity made no sense. The first was an alfalfa-breeding model with two numeric predictors and two dummy variables. The second was an economic model with one numeric predictor, one dummy and the numeric x dummy cross-product. This paper gives formulas for VIFs for several regression models with a dummy variable which indicate that these VIFs are functions of the numeric predictors\u27 means, sums of squares and sample sizes within the two dummy groups. The economic regression model is also presented to illustrate how high VIFs occurred in this data. Researchers should be cautious in using high VIFs as a reason for deleting predictors in general but especially if dummy variables are involved. It is recommended that collinearity diagnostics be applied to the numeric predictors first to check for collinearity without the influence of any dummies, then add dummy variables in one at a time to see their effect on VIFs

Use of Temperature, Humidity, and Slaughter Condemnation Data to Predict Increases in Transport Losses in Three Classes of Swine and Resulting Foregone Revenue

The United States Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) conducts weekly surveillance of slaughter condemnation rates to provide early warning for emerging diseases and to monitor health trends in swine. Swine deaths in-transit are an animal welfare concern and represent lost revenue for the swine industry. This retrospective observational study used ambient temperature and humidity data from weather stations near United States slaughter plants collected from 2010 to 2015 to predict the incidence and risk of death among swine in-transit and just prior to slaughter. The risk of death for market swine at a heat index (HI), which combines the effects of temperature and humidity, indicating moderately hot weather conditions between 85 and 92°F was 1.37 times greater than that of the baseline temperature range of 54–79°F. The risk of death for cull sows at an HI between 85 and 92°F was 1.93 times greater than that of average temperatures ranging from 54 to 79°F. Roaster swine (weigh < 220 lbs and often used for whole carcass roasting), however, had 0.80 times the risk when the HI was 85–92°F compared to a baseline temperature of 54–79°F. The risk of death for roaster swine at a minimum temperature between 40 and 50°F was 1.21 times greater than that of average temperatures ranging from 54 to 79°F. The risk of death for market swine at a minimum temperature range of 40–50°F was 0.97 times that of average temperatures ranging from 54 to 79°F. And for cull sows, the risk of death at a minimum temperature range of 40–50°F was 0.81 times the risk at the average temperature ranging from 54 to 79°F. Across the study period, cumulative foregone revenue, or revenue not realized due to swine condemnations, for all swine was $18.6 million and$4.3 million for cold temperatures and high HI ranges above the baseline, respectively. Marginal foregone revenue per hog in hotter months is higher due to seasonal peaks in swine prices. As a result of this study, the USDA-APHIS swine condemnation surveillance can incorporate weekly estimated HI values and ambient temperature data for slaughter establishments to provide additional information for analysts investigating signals (noteworthy increases above baseline) for “dead” condemnations. This study suggests that current mitigation measures are often not sufficient to prevent swine deaths due to ambient temperature extremes

Using a Portfolio Approach to Evaluate Animal Health Surveillance Portfolios in the United States

Selecting the optimal level of surveillance to implement for an animal disease is important when decision-makers are allocating resources within a surveillance portfolio (collection of all surveillance activities for a species). Decision-makers should consider economically efficient options that meet effectiveness requirements of a surveillance system (i.e., disease detection capability, timeliness, etc.). In this research, we look at components in two disease surveillance systems within a species portfolio and compare current surveillance testing levels with four other optional levels. Option 1 does not meet the detection capability thresholds, while option 2 meets thresholds for one disease but not the other. Options 3 and 4 meet the detection capability thresholds and result in a cost savings compared to current levels. We conclude that Option 3 would be the optimum level of surveillance as it has a lower cost-effectiveness ratio compared to option 4 and the current level, as well as a cost savings of $637,500

Pen-Based Swine Oral Fluid Samples Contain Both Environmental and Pig-Derived Targets

Laboratory methods for detecting specific pathogens in oral fluids are widely reported, but there is little research on the oral fluid sampling process itself. In this study, a fluorescent tracer (diluted red food coloring) was used to test the transfer of a target directly from pigs or indirectly from the environment to pen-based oral fluid samples. Pens of ~30, ~60, and ~125 14-week-old pigs (32 pens/size) on commercial swine farms received one of two treatments: (1) pig exposure, i.e., ~3.5 mL of tracer solution sprayed into the mouth of 10% of the pigs in the pen; (2) environmental exposure, i.e., 20 mL of tracer solution was poured on the floor in the center of the pen. Oral fluids collected one day prior to treatment (baseline fluorescence control) and immediately after treatment were tested for fluorescence. Data were evaluated by receiver operating characteristic (ROC) analysis, with Youden’s J statistic used to set a threshold. Pretreatment oral fluid samples with fluorescence responses above the ROC threshold were removed from further analysis (7 of 96 samples). Based on the ROC analyses, oral fluid samples from 78 of 89 pens (87.6%), contained red food coloring, including 43 of 47 (91.5%) pens receiving pig exposure and 35 of 42 (83.3%) pens receiving environmental exposure. Thus, oral fluid samples contain both pig-derived and environmental targets. This methodology provides a safe and quantifiable method to evaluate oral fluid sampling vis-à-vis pen behavior, pen size, sampling protocol, and target distribution in the pen

Viability of African Swine Fever Virus with the Shallow Burial with Carbon Carcass Disposal Method

African swine fever (ASF) is a highly contagious swine disease with high mortality. In many countries, culling pigs infected and exposed to the ASF virus is mandatory to control the disease, which poses a real challenge in the disposal of large numbers of carcasses during ASF outbreaks. Shallow burial with carbon (SBC) Thanks ew mortality disposal method developed from deep burial and composting. The present study investigates the effectiveness of SBC in disposing of ASF virus-infected pigs. The real-time PCR results showed that DNA of the ASF virus was still detected in bone marrow samples on day 56, while the virus isolation test revealed that the infectious ASF virus was destroyed in both spleen and bone marrow samples on day 5. Interestingly, decomposition was found to occur rapidly in these shallow burial pits. On day 144, only large bones were found in the burial pit. In general, the results of this study indicated that SBC is a potential method for the disposal of ASF-infected carcasses; however, further studies are needed to provide more scientific evidence for the efficacy of SBC in different environment conditions